GtUword greedyunitedist(GtFrontResource *ftres,
const GtSeqabstract *useq,
const GtSeqabstract *vseq)
{
GtUword realdistance, kval;
GtWord r;
GtFrontspec frontspecspace[2], *fspec, *prevfspec;
GtFrontvalue *fptr;
#ifdef SKDEBUG
printf("unitedistcheckSEPgeneric(ulen=" GT_WU ",vlen=" GT_WU ")\n",
ulenvalue,vlenvalue);
#endif
gt_assert(gt_seqabstract_length(useq) < (GtUword) LONG_MAX);
gt_assert(gt_seqabstract_length(vseq) < (GtUword) LONG_MAX);
ftres->ulen = (GtWord) gt_seqabstract_length(useq);
ftres->vlen = (GtWord) gt_seqabstract_length(vseq);
ftres->integermin = -MAX(ftres->ulen,ftres->vlen);
prevfspec = &frontspecspace[0];
firstfrontforward(useq,vseq,ftres,prevfspec);
if (ftres->ulen == ftres->vlen &&
GT_FRONT_ROWVALUE(ftres->frontspace) == ftres->vlen)
{
realdistance = 0;
} else
{
for (kval=1UL, r=1-MIN(ftres->ulen,ftres->vlen);
/* Nothing */ ; kval++, r++)
{
if (prevfspec == &frontspecspace[0])
{
fspec = &frontspecspace[1];
} else
{
fspec = &frontspecspace[0];
}
fspec->offset = prevfspec->offset + prevfspec->width;
frontspecparms(ftres,fspec,(GtWord) kval,r);
while ((GtUword) (fspec->offset + fspec->width)
>= ftres->currentallocated)
{
ftres->currentallocated += kval+1;
ftres->frontspace
= gt_realloc(ftres->frontspace,
sizeof *ftres->frontspace * ftres->currentallocated);
}
(void) evalfrontforward(useq,vseq,ftres,prevfspec,fspec,r);
fptr = ftres->frontspace + fspec->offset - fspec->left;
if (accessfront(ftres,fptr,fspec,ftres->vlen - ftres->ulen)
== ftres->ulen)
{
realdistance = kval;
break;
}
if (prevfspec == &frontspecspace[0])
{
prevfspec = &frontspecspace[1];
} else
{
prevfspec = &frontspecspace[0];
}
}
}
#ifdef SKDEBUG
printf("unitedistfrontSEP returns "GT_WD"\n",realdistance);
#endif
return realdistance;
}
unsigned long greedyunitedist(const GtUchar *useq,
unsigned long ulenvalue,
const GtUchar *vseq,
unsigned long vlenvalue)
{
unsigned long currentallocated, realdistance;
FrontResource gl;
Frontspec frontspecspace[2],
*fspec,
*prevfspec;
Frontvalue *fptr;
unsigned long kval;
long r;
#ifdef SKDEBUG
printf("unitedistcheckSEPgeneric(ulen=%lu,vlen=%lu)\n",ulenvalue,vlenvalue);
#endif
gt_assert(ulenvalue < (unsigned long) LONG_MAX);
gt_assert(vlenvalue < (unsigned long) LONG_MAX);
currentallocated = 1UL;
ALLOCASSIGNSPACE(gl.frontspace,NULL,Frontvalue,currentallocated);
gl.useq = useq;
gl.vseq = vseq;
gl.ubound = useq + ulenvalue;
gl.vbound = vseq + vlenvalue;
gl.ulen = (long) ulenvalue;
gl.vlen = (long) vlenvalue;
gl.integermin = -MAX(gl.ulen,gl.vlen);
prevfspec = &frontspecspace[0];
firstfrontforward(&gl,prevfspec);
if (gl.ulen == gl.vlen && ROWVALUE(&gl.frontspace[0]) == gl.vlen)
{
realdistance = 0;
} else
{
for (kval=1UL, r=1-MIN(gl.ulen,gl.vlen); /* Nothing */ ; kval++, r++)
{
if (prevfspec == &frontspecspace[0])
{
fspec = &frontspecspace[1];
} else
{
fspec = &frontspecspace[0];
}
fspec->offset = prevfspec->offset + prevfspec->width;
frontspecparms(&gl,fspec,(long) kval,r);
while ((unsigned long) (fspec->offset + fspec->width)
>= currentallocated)
{
currentallocated += (kval+1);
ALLOCASSIGNSPACE(gl.frontspace,gl.frontspace,
Frontvalue,currentallocated);
}
(void) evalfrontforward(&gl,prevfspec,fspec,r);
fptr = gl.frontspace + fspec->offset - fspec->left;
if (accessfront(&gl,fptr,fspec,gl.vlen - gl.ulen) == gl.ulen)
{
realdistance = kval;
break;
}
if (prevfspec == &frontspecspace[0])
{
prevfspec = &frontspecspace[1];
} else
{
prevfspec = &frontspecspace[0];
}
}
}
#ifdef SKDEBUG
printf("unitedistfrontSEP returns %ld\n",realdistance);
#endif
FREESPACE(gl.frontspace);
return realdistance;
}
static void evalentryforward(const GtSeqabstract *useq,
const GtSeqabstract *vseq,
GtFrontResource *ftres,
GtFrontvalue *fval,
const GtFrontspec *fspec,
GtWord k)
{
GtWord value, t;
GtFrontvalue *fptr;
#ifdef SKDEBUG
printf("evalentryforward(k="GT_WD")\n",k);
#endif
fptr = ftres->frontspace + fspec->offset - fspec->left;
t = accessfront(ftres,fptr,fspec,k) + 1; /* same diagonal */
#ifdef SKDEBUG
printf("same: access(k="GT_WD")="GT_WD"\n",k,t-1);
#endif
value = accessfront(ftres,fptr,fspec,k-1); /* diagonal below */
#ifdef SKDEBUG
printf("below: access(k="GT_WD")="GT_WD"\n",k-1,value);
#endif
if (t < value)
{
t = value;
}
value = accessfront(ftres,fptr,fspec,k+1) + 1; /* diagonal above */
#ifdef SKDEBUG
printf("above: access(k="GT_WD")="GT_WD"\n",k+1,value-1);
#endif
if (t < value)
{
t = value;
}
#ifdef SKDEBUG
printf("maximum: t="GT_WD"\n",t); /* the maximum over three values */
#endif
if (t < 0 || t+k < 0) /* no negative value */
{
GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),GT_FRONT_MINUSINFINITY(ftres));
} else
{
if (ftres->ulen != 0 && ftres->vlen != 0 &&
t < ftres->ulen && t + k < ftres->vlen)
{
GtUword lcp, minlen
= (GtUword) MIN(ftres->ulen - t,ftres->vlen - (t + k));
lcp = gt_seqabstract_lcp(true,
useq,
vseq,
(GtUword) t,
(GtUword) (t + k),
minlen);
t += lcp;
}
if (t > ftres->ulen || t + k > ftres->vlen)
{
GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),
GT_FRONT_MINUSINFINITY(ftres));
} else
{
GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),t);
}
}
}
static void evalentryforward(FrontResource *gl,
Frontvalue *fval,
const Frontspec *fspec,
long k)
{
long value, t;
const GtUchar *uptr, *vptr;
GtUchar a, b;
Frontvalue *fptr;
#ifdef SKDEBUG
printf("evalentryforward(k=%ld)\n",k);
#endif
fptr = gl->frontspace + fspec->offset - fspec->left;
t = accessfront(gl,fptr,fspec,k) + 1; /* same diagonal */
#ifdef SKDEBUG
printf("same: access(k=%ld)=%ld\n",k,t-1);
#endif
value = accessfront(gl,fptr,fspec,k-1); /* diagonal below */
#ifdef SKDEBUG
printf("below: access(k=%ld)=%ld\n",k-1,value);
#endif
if (t < value)
{
t = value;
}
value = accessfront(gl,fptr,fspec,k+1) + 1; /* diagonal above */
#ifdef SKDEBUG
printf("above: access(k=%ld)=%ld\n",k+1,value-1);
#endif
if (t < value)
{
t = value;
}
#ifdef SKDEBUG
printf("maximum: t=%ld\n",t); /* the maximum over three values */
#endif
if (t < 0 || t+k < 0) /* no negative value */
{
STOREFRONT(gl,ROWVALUE(fval),MINUSINFINITYFRONT(gl));
} else
{
uptr = gl->useq + t;
vptr = gl->vseq + t + k;
if (gl->ulen != 0 && gl->vlen != 0) /* only for nonempty strings */
{
if (uptr == vptr) /* strings are equal */
{
t = gl->ulen-1;
} else
{
for (/* Nothing */; uptr < gl->ubound && vptr < gl->vbound;
uptr++, vptr++)
{
a = *uptr;
b = *vptr;
COMPARESYMBOLS(a,b);
}
t = (long) (uptr - gl->useq);
}
}
if (gl->useq + t > gl->ubound || gl->vseq + t + k > gl->vbound)
{
STOREFRONT(gl,ROWVALUE(fval),MINUSINFINITYFRONT(gl));
} else
{
STOREFRONT(gl,ROWVALUE(fval),t);
}
}
}
